Do the tokens that are going to be used by the connected players have to be on there machine or will they be sent over the connection once there on the map. Also can you setup a map ahead of time with NPC's and such and have them hidden from the player
Tokens can actually be added by any client (including the GM) and everybody will get a copy. The nice thing is that the token image is then stored on each machine and doesn't need to be retransmitted each time you start up, which works great for multiple-session campaigns.
You can certainly set up your campaign early. Start up MapTool, load your maps, add the tokens, then File->Save Campaign. When it is time to play, just File->Load Campaign and pick your saved campaign.
It is recommended that you do a Server->Start Server while you work on your campaign, this seems to work best while we're tightening the nuts and bolts.
Fog of War and token visibility were just added over the past week, so you can set up quite a bit and hided it behind a fog of war.
As a side note, fog of war is still in early development. It has the basic functionality, but still needs usability tweaks.
Very cool, I will test them out and post when done.